Keith was likely the first to detect signs of Heart and Skeletal Muscle Inflammation. The disease, first found three years earlier in Norwegian farmed salmon, went on to plague the industry there, killing up to 20 per cent of salmon in some outbreaks.

Yet for the next 14 years, working closely with the industry and the provincial lab that audits fish farm health, the DFO went to great lengths to avoid acknowledging HSMI’s presence in B.C. waters.

That’s not surprising. Justice Bruce Cohen warned DFO had a fundamental conflict in his 2012 report on disappearing Fraser River sockeye.

“When DFO has simultaneous mandates to conserve wild stocks and promote the salmon farming industry, there are circumstances in which it can find itself in a conflict of interest because of divided loyalties.”

And after reviewing hundreds of pages of academic papers, court transcripts, sworn affidavits and internal emails obtained by The Tyee, it is clear just how deep this unresolved conflict goes.

HSMI was hardly flying below the radar. By 2004, Norwegian scientists were publishing research and establishing a diagnostic framework for the disease.

But in B.C. — where the provincial agriculture ministry oversaw fish farms until 2009 — government veterinarians worked closely with the industry they were charged with auditing and developed their own diagnosis of HSMI. It allowed both to deny the existence of the disease in B.C. waters for years.

Dr. Gary Marty was the key provincial figure in the denial that HSMI exists in B.C. waters. A veterinarian with a PhD in comparative pathology, Marty is senior fish pathologist at the B.C. government’s Animal Health Centre in Abbotsford and oversees a small team responsible for quarterly audits of the health of B.C.’s farmed salmon. Field monitoring is done by the industry’s own veterinarians, with DFO’s Fish Health Audit and Surveillance program making the occasional site visit and collecting dead fish, called “silvers,” to pass along to Marty’s lab for analysis. (They do not sample any live fish.)

The Animal Health Centre receives $7 million in funding from the province’s agriculture ministry and about $1.4 million from clients — including $176,000 from three salmon aquaculture companies in the latest fiscal year. It’s also under contract with the DFO to perform farmed salmon audits.

Even after a 2009 court ruling forced the federal government to take over regulation of fish farms, the feds contracted with Marty’s lab to continue providing diagnostic services. The DFO did not, however, provide any direction to AHC on the specific diagnostic methods it had to use to assess viruses and diseases.

And the lab’s approach has come under criticism from other scientists for “errors of interpretation and a selective use of the literature” and a bias favouring salmon farms — and scrutiny from the new provincial government.

In October, the controversy became public when long-time DFO scientist Dr. Kristi Miller raised questions about perceptions of conflict of interest in a report by CTV’s W5 that led to an ongoing provincial government investigation into Marty’s lab.

“He has a relationship with the industry and he also is the person doing the pathology associated with the regulatory programs,” Miller said. “Even if it isn’t a conflict of interest, it has the appearance of one.”

Marty agreed that he works closely with industry veterinarians. “If we have a good relationship with our industry, if they trust us, they will provide us with samples of dead fish,” he said.

The industry — and Marty — have long denied HSMI is present in farmed salmon in B.C. waters. In 2013, in a report used by Marine Harvest, Marty was clear: “HSMI does not occur in B.C.” The Norwegian-based global corporation is the largest fish farm operator in B.C. waters.

But the 2012 Cohen Commission report had included a recommendation for more testing for diseases associated with wild and farmed fish. As a result, the Strategic Salmon Health Initiative was launched, a joint project of the Pacific Salmon Foundation, DFO and Genome BC, with Miller playing a key role.

Using leading-edge genomic testing methods, Miller and her colleagues found HSMI and PRV in fish sampled from a farm in the Okisollo Channel between 2013 and 2014.

It’s an important discovery, as recent research indicates. A recent studyestablished that HSMI is caused by piscine reovirus, which is prevalent in farmed salmon. Another research report found PRV, also found in wild salmon, may reduce their ability “to complete a challenging upriver migration” and spawn. And in a 2015 decision, Federal Court Judge Donald Rennie found PRV likely causes HSMI and “may be harmful to the protection and conservation of [wild] fish.”

It would take a couple years of due diligence — double blind testing with several labs and verification by an interdisciplinary team of eight scientists from Canada, Norway and Scotland — before the researchers were ready to make their findings public.

But what should have been a simple scientific announcement quickly became the centre of a political battle. Dozens of internal emails and revisions to communications documents show just how much pressure came to bear on Miller’s team from DFO management and the industry lobby to downplay their findings.

As of May 10, 2016, with the scheduled announcement of the findings less than two weeks away, a draft DFO news release was titled “HSMI Detected in B.C. Farmed Fish.”

On May 17, three days before the release was to be distributed, a series of emails reveal the internal struggle over the news release. DFO officials qualify the findings by adding the word “preliminary” to describe them.

Miller wrote to Dan Bate, DFO’s team lead for strategic communications, Pacific region, objecting to the fact that the qualifier had been added to the release.

“We had already edited, but the term preliminary was reinserted.”

Miller argued the release should be headlined “first diagnosis” of HSMI in B.C. without ambiguity.

Bate told her he would forward her concerns, but by that point in the day he had already received approval from regional director general Rebecca Reid for the version containing “preliminary.”

DFO’s Wayne Moore, director general of the strategic and regulatory science directorate, waded into the fray on May 19.

“When I look at the ICES fact sheet on HSMI it would seem to support Kristi and her team’s view that a diagnosis of HSMI is based on a histological examination of changes in heart and skeletal muscle,” Moore wrote. “No discussion about other clinical signs.” (ICES — the International Council for the Exploration of the Sea — is a network of more than 5,000 scientists from over 690 marine institutes in 20 member countries.)

But Dr. Simon Jones, lead scientist in the finfish parasitology program at DFO’s Pacific Biological Station — the same facility where Miller’s SSHI lab is based — disagreed. “I’d be cautious about drawing conclusions from any one article, especially if it’s misquoted or inadequately quoted.”

Yet the ICES document summarized years of published research and set out a standard framework for diagnosis in order to avoid the very confusion now surrounding Miller’s findings.

Other emails, like one on May 18 from Heather Wood, DFO’s regional manager of aquaculture programs, reveal industry influence on the announcement.

“I have been in frequent contact with Comms and we have sent forward some tweaks to the [news release] to accommodate concerns from both DFO science, vets and industry, following today’s discussion — hopefully that is the version that will be released on Friday morning.”

She also wrote: “We are being asked by industry — how will DFO respond?.... I expect industry will be looking to us immediately on what this means going forward.”

Miller lost the battle. The final version of the release that went out on May 20 was headlined “Potential Diagnosis of Heart and Skeletal Muscle Inflammation in Atlantic Salmon at a B.C. Fish Farm.”

The same day, the BC Salmon Farmers Association put out its own advisory further undermining the announcement. “There is no consensus amongst the scientific community about the findings as the fish sampled in this farm showed no clinical signs of disease,” it declared.

Strategic Salmon Health Initiative program head Brian Riddell forwarded the industry statement to Miller, asking “Does this contradict what you have said re: finding disease HSMI?”

Miller responded firmly.

“The disease HSMI is diagnosed based on pathology, not clinical signs — that is the international standard,” she wrote. “Our study not only showed that the pathology was highly diagnostic of HSMI (note our lead pathologist, Hugh Ferguson, was the first pathologist to describe this disease in Scotland.... He is absolutely sure about this being HSMI, as are the Norwegians we consulted to conduct the Immunohistochemistry, both experts on this disease... ”

The initiative’s own draft communications plan makes it clear what they were up against, noting: “both [DFO] and the aquaculture companies have previously vehemently denied that HSMI is present in B.C. fish farms... Dr. Gary Marty is the lead pathologist for the DFO regulatory program and the industry.”

Internal emails and communication documents show Marty’s work was the foundation for the battle to downplay the HSMI findings.

Three days after the announcement, he sent critical emails to Miller and her colleagues.

“I do not want SSHI to be seen as a project that takes credit for discoveries that were previously reported by other scientists,” he wrote. “My understanding is that the SSHI team confirmed the presence of a disease that has long been detected in B.C. And, microscopic features of the 2013 outbreak reported by DFO last Friday were first reported publicly by another researcher (me) in 2013.”

But Marty chose not to use the term HSMI in his reports, often referring to it as a “heart disease of unknown cause.” In a 2016 email, he described his findings as IHSM (inflammation in the heart and skeletal muscle).

When asked about HSMI by Justine Hunter of the Globe and Mail, Marty dismissed the matter as a mere trifle over a name.

“The heart disease is not new to B.C., just the name,” he said. “Changing the name of a disease is not a threat to wild salmon.”

But Marty did more than not use the disease name.

In January 2016, he co-published a paper in PLOS One with four DFO scientists and Diane Morrison, an employee of Marine Harvest, which partially funded the paper.

In it they state several times that “there is no known occurrence of HSMI” in western North America. But their research used a narrower — and harder to establish — definition of HSMI than Miller and other published scientists use.

They did not disclose this in their paper. When I asked Marty if they should have made this disclosure, he replied that their diagnostic approach is based on a 2007 paper by M.F. McLoughlin and D.A. Graham in the Journal of Fish Diseases, which he says argues for “a combination of clinical signs, gross [pathology] and histopathology....” in diagnosing HSMI.

I put this response to Dr. Emiliano Di Ciccio, co-author of the initiative’s paper on HSMI, who said Marty misinterpreted or mis-cited McLoughlin’s report, which focused on salmon pancreas disease.

“It’s evident that, in the sentence reported by Dr. Marty, the authors clearly refer to PD,” he said, not HSMI.

The crux of the dispute is simple. The first major paper on HSMI, by Kongtorp et al in 2004, established the diagnostic model for the disease which was also set out in the 2012 de facto manual on HSMI diagnosis by Biering and Garseth for ICES.

Miller and her colleagues noted in their published findings in PLOS One in February 2017 they used “the international standard of specific pathological lesions in heart and skeletal tissues as the case definition for HSMI.”

But Marty disputes that definition. In an emailed response to my questions, he maintained, “their paper does not cite any reference that establishes the ‘international standard.’”

Marty made the same argument in an email to Miller’s research team after their findings were released.

“The SSHI team seems to be using a case definition for HSMI that is different from the HSMI case definition used over the past decade by the BC veterinarians, which could be stated in this way:

“BC veterinarians — HSMI is diagnosed based on characteristic abnormalities in the heart and muscle, AND characteristic clinical signs (e.g. fish are lethargic, eat poorly, and growth is slower than normal).

“SSHI — HSMI is diagnosed based on characteristic abnormalities in the heart and muscle.”

Marty and his provincial lab colleagues required not just evidence of HSMI in the fish, but behavioural observations like slow growth.

Marty confirmed this in another email on May 21, 2016, to two of Miller’s colleagues, which also highlighted the reliance on industry employees.

“The aquaculture veterinarians said they were not seeing a clinical pattern that was consistent with Norwegian HSMI.... ” he wrote. “Therefore, we decided what I was seeing was probably not the same as Norwegian HSMI.”

Yet other scientists who work on the disease, backed up by the scientific literature on the subject, do not require clinical signs for the diagnosis of HSMI. A 2006 paper by Kongtorp et al — the same group that pioneered the diagnosis of HSMI — explained why clinical signs are a red herring: “There was no evident difference in lesion severity in fish showing clinical signs compared with those behaving normally.”

In other words, fish can carry the disease without showing outward symptoms, depending on a host of factors. As Dr. Di Ciccio explains, “We know that fish carrying HSMI heart lesions (even severe lesions) can or cannot show clinical signs or mortality even in the field,” Di Ciccio explained. Stressful events — like variations in temperature, salinity, dissolved oxygen, harmful algae blooms, sea lice or handling — can lead to the symptoms, he said.

Marty and the industry insist that mortality rates are too low on B.C.’s farms to be caused by HSMI, yet they attribute many deaths to the above sorts of “environmental conditions.”

I asked Marty if relying on the observations of the industry’s own veterinarians as part of his diagnosis creates the risk of a conflict of interest.

“‘Best practices’ in diagnostic medicine are achieved when licensed practitioners — experts in the health of their patients — send samples to accredited laboratories staffed by specialists in diagnostic pathology,” he replied in an email.

Marty has acknowledged that he started seeing “HSMI-like” heart lesions in 2004, when he began his tenure at the Animal Health Centre. But he says he didn’t realize they were consistent with Norwegian HSMI until a conference he attended in 2008.

But the HSMI battle shows how deeply entrenched the promotion and protection of the aquaculture industry remains within the federal bureaucracy — and how far we are from resolving the conflict of interest Cohen warned about.

Yet there are signs of change provincially. The NDP government, responsible for Marty’s lab and the ocean tenures the industry requires to operate, has three reviews under way. It’s examining the practice of discharging blood and waste from fish processing plants into the marine environment; the use of harmful pesticides to treat parasites on the farms; and the Animal Health Centre’s operations.

Pressure from First Nations played an important role. In a visit to Alert Bay on Oct. 10, Premier John Horgan told First Nations the government shared their concerns about open net fish farms. And he agreed that fish farms facing tenure renewals — many of them set for this June — should not be restocking their pens. Later that week, Marine Harvest would restock its Port Elizabeth farm anyway, with RCMP assistance, in the face of a First Nations protest.

Agriculture Minister Lana Popham had sent the company a sharply worded letter on Oct. 13.

“The decision to restock occurs as we are entering into sensitive discussions with some of the First Nations in the Broughton Archipelago who remain opposed to open net pen salmon farming in their territories,” she wrote. “Our government has committed to implementing the United Nations Declaration on the Rights of Indigenous People.... Whatever operational decisions you should choose to make, the province retains all of its rights under the current tenure agreements, including potentially the requirement that you return possession of tenured sites at the end of the current terms.”

Popham was pilloried in the media and legislature for putting a “chill” on business throughout the province. Vancouver Sun columnist Vaughn Palmer wrote that she had sent an “eviction notice-like letter” to the industry.

Yet Popham’s letter also told the companies that officials “will be in touch with you to describe the process for you to initiate applications for replacement tenures... we look forward to your input on the lease renewal decisions.” The government has since accepted applications for tenure renewals, but has yet to rule on them.

Despite the attacks on Popham and the NDP from the media and business leaders like Greg D’Avignon, president of the B.C. Business Council and former executive director of the BC Salmon Farmers Association, Horgan stood behind the investigation into Marty’s lab, assigning the job to his deputy minister Don Wright.

The review, the government says, will not look at the actions of individuals. Marty told the Vancouver Sun “I’ve heard the minister say there is no concern about my job. I’m in a unionized position. Realistically, it would be nearly impossible for me to be fired.”

But the investigation will explore whether “best practices and ethical standards are followed, including protecting against potential conflicts of interest,” which could spell change for the lab and industry.

A source close to the review suggests the government is aiming to have a report this month.